Update mcp/cbio.py

mcp/cbio.py

@@ -1,36 +1,14 @@
-import logging
+# mcp/cbio.py
+from functools import lru_cache
+from mcp.clients import BaseClient
 
-# Try to import the official pybioportal client; if it isn't installed, we'll disable cBio queries.
-try:
-    from pybioportal import fetch_muts_in_multiple_mol_profs, fetch_molecular_profiles
-    _CBIO_ENABLED = True
-except ImportError:
-    logging.warning("pybioportal package not available; disabling cBioPortal integration")
-    _CBIO_ENABLED = False
+class CbioClient(BaseClient):
+    def __init__(self):
+        super().__init__("https://www.cbioportal.org/api", None)
 
-async def fetch_cbio(gene: str) -> list:
-    """
-    Fetch cancer variant data for the given gene from cBioPortal.
-    Returns an empty list if pybioportal isn't installed or on any error.
-    """
-    if not _CBIO_ENABLED:
-        return []
+    @lru_cache(256)
+    async def fetch_variants(self, gene: str, profile: str="brca_tcga_pan_can_atlas_2018_mutations"):
+        path = f"molecular-profiles/{profile}/genes/{gene}/mutations?projection=SUMMARY"
+        return await self.request("GET", path)
 
-    try:
-        # 1) Grab all molecular profiles (you can restrict to particular studies if you like)
-        profiles = fetch_molecular_profiles()  # returns list of dicts with 'molecular_profile_id', etc.
-
-        # 2) For each profile, fetch the mutations for our gene
-        variants = []
-        for prof in profiles:
-            mpid = prof.get("molecular_profile_id")
-            if mpid:
-                # fetch_muts_in_multiple_mol_profs returns a list of mutation dicts
-                muts = fetch_muts_in_multiple_mol_profs([mpid], gene=gene)
-                variants.extend(muts or [])
-
-        return variants
-
-    except Exception as e:
-        logging.warning("cBioPortal variant fetch failed: %s", e)
-        return []
+cbio = CbioClient()